Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes

To assess the physico-chemical characteristics of protein-protein interactions, protein sequences and overall structural folds have been analyzed previously. To highlight this, discovery and examination of amino acid patterns at the binding sites defined by structural proximity in 3-dimensional (3D) space are essential. In this paper, we investigate the interacting preferences of 3D pattern pairs discovered separately in transient and obligate protein complexes. These 3D pattern pairs are not necessarily sequence-consecutive, but each residue in two groups of amino acids from two proteins in a complex is within certain °A threshold to most residues in the other group. We develop an algorithm called AA-pairs by which every pair of interacting proteins is represented as a bipartite graph, and it discovers all maximal quasi-bicliques from every bipartite graph to form our 3D pattern pairs. From 112 and 2533 highly conserved 3D pattern pairs discovered in the transient and obligate complexes respectively, we observe that Ala and Leu is the highest occuring amino acid in interacting 3D patterns of transient (20.91%) and obligate (33.82%) complexes respectively. From the study on the dipeptide composition on each side of interacting 3D pattern pairs, dipeptides Ala-Ala and Ala-Leu are popular in 3D patterns of both transient and obligate complexes. The interactions between amino acids with large hydrophobicity difference are present more in the transient than in the obligate complexes. On contrary, in obligate complexes, interactions between hydrophobic residues account for the top 5 most occuring amino acid pairings.

There is something about pairs trading

The process of pairs trading involves exhaustively matching and ranking pairwise stocks based on some prespecified measure of closeness; e.g., correlation, cointegration, sum-of-squared price difference. Pairs trading is popular for various reasons. It is simple to follow and execute. The pairwise portfolio can be nearly market-neutral, such that it does not require the comprehensive analysis of macroeconomic news. Since it is based on relative valuation, the actual worth of individual firms is not a pertinent consideration. The strategy is sufficiently flexible to accommodate various investment styles. Lastly, it does not evoke frequent intraday rebalancing, such that pairs trading can be automated to a certain extent and be cost-feasibly profitable. Despite its long history on Wall Street, pairs trading remains elusive in nature. The academic attention it attracts is modest compared to contrarian and momentum trading.

Genetic and environmental influences on variation in balance performance among female twin pairs aged 21-82 years

Genetic and environmental influences on variation in balance performance were measured in 93 monozygous and 83 dizygous female twin pairs aged 21–82 years (mean age, 50.5 years) in Melbourne, Australia, between 1999 and 2003. The authors administered clinical (Lord's Balance Test and Step Test) and laboratory tests of static and dynamic balance from the Chattecx Balance System with and without distractor tasks. The authors conducted factor analysis and estimated genetic and environmental variance components and heritability (defined as additive genetic variance as a proportion of all variance, after adjustment for age) using a multivariate normal model with the statistical package FISHER. Three factors were identified and adjusted for age. Heritability was 46% (standard error (SE), 9) for the "sensory balance tests" factor and 30% (SE, 9) for the "static and dynamic perturbations" factor. For both factors, the remaining variance was attributed to unique environmental effects. There was no evidence that genetic factors influenced variation in the "dynamic weight shift tests" factor, with environmental effects shared by twins accounting for 38% (SE, 7) of variance. Neither genetic nor environmental proportions of variance differed significantly between twin subgroups by age (≤50/>50 years). An age-related decline in performance measures was found across the whole sample. These results imply that balance impairments may have a heritable element.

Liquids intermediate between 'molecular' and 'ionic' liquids : liquid ion pairs?

Ionic liquids comprised of tetradecyltrihexyl- and tetrabutyl- phosphonium cations paired with chloride or sulfonyl amide anions exhibit properties that reflect strong ion association, including comparatively low viscosity as well as a degree of volatility, and hence exemplify an interesting intermediate state between true ionic and true molecular liquids.

ATR FT-IR absorption enhancement of a thin film under the photon-tunneling condition

A simple, yet very powerful technique for the spectral acquisition of an extremely thin film with enhanced absorption was explored. An infrared absorption of an extremely thin film confined between media of high refractive indices was greater than that of its bulk when the spectrum was acquired under the attenuated total reflection (ATR) condition with parallel (p) polarized radiation. The absorption enhancement was not observed under perpendicular (s) polarized radiation. Theoretical investigations indicated that the absorption enhancement was proportional to the integration of the mean square evanescent field within the film. The field integration under p-polarized radiation increased, while that under s-polarized radiation decreased as the thickness of the confined film became thinner. The maximum enhancement was observed when the film was sufficiently thinner than the penetration depth. The phenomena were experimentally investigated, and the results agreed very well with theoretical predictions.

An analysis of side chain interactions and pair correlations within antiparallel β-sheets : the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs

Cross-strand pair correlations are calculated for residue pairs in antiparallel β-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. Thestrongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β- and γ-branched residues inthe non-H-bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded β- and γ-branched residue pairs, (2) the handedness of the observed enantiomers of chiral β-branched side chains, and (3) the handedness of the twist of β-sheet. These findings have implications for the formation of β-sheets during protein folding and the mechanism by which the sheet becomes twisted

Two-photon endomicroscopy for 3D imaging of cancer cells labelled with gold nanorods

Biofunctional nanorods are developed to specifically target cancer cells. The cervical cancer cells, HeLa cells, are labeled by these biofunctional gold nanorods. Those cancer cells can be detected by a multi-photon-excited photoluminescence endomicroscope, which proves that the cancers can be in vivo diagnosed by using biofunctional gold nanorods with nonlinear endomicroscopy.

Two-photon imaging and photothermal therapy of cancer cells using biofunctional gold nanorods

Transferrin-conjugated gold nanorods were used for targeting, two-photon imaging and photothermal therapy of cancer cells. The presence of nanorods significantly reduced the laser power effective for therapy.

Computational modeling aspects of photon transport equations in biological media

This paper presents an overview of modeling light propagation through biological media by solving the photon transport equation. Different variants of the photon transport equation (PTE) are discussed. Several methods for modeling static distributions and the transient response are presented. A discussion on how to mix and match electromagnetic problems with the PTE is also provided.

Conformational changes in redox pairs of protein structures

Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox-active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity.